I am having some troubles when running MFiX 23.4 in a remote computer. I have tried with both Miniforge3 and Anaconda3. I have followed the same steps as usual for the installation. However, I am finding the following issues:
If I compile from terminal I have no problem and mfixsolver_dmp is compiled. However, I am finding the following error message:
Traceback (most recent call last):
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/runpy.py”, line 196, in _run_module_as_main
Traceback (most recent call last):
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/runpy.py”, line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/runpy.py”, line 86, in _run_code
return _run_code(code, main_globals, None,
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/runpy.py”, line 86, in _run_code
exec(code, run_globals)
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/site-packages/mfix_solver/pymfix.py”, line 373, in
exec(code, run_globals)
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/site-packages/mfix_solver/pymfix.py”, line 373, in
main()
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/site-packages/mfix_solver/pymfix.py”, line 280, in main
main()
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/site-packages/mfix_solver/pymfix.py”, line 280, in main
M = ctypes.CDLL(so_path)
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/ctypes/init.py”, line 374, in init
M = ctypes.CDLL(so_path)
File “/home/edu/anaconda3/envs/mfix-23.4/lib/python3.10/ctypes/init.py”, line 374, in init
self._handle = _dlopen(self._name, mode)
self._handle = _dlopen(self._name, mode)
OSError: /DATOS/home/edu/anaconda3/envs/mfix-23.4/bin/…/lib/libmpi_mpifh.so.40: undefined symbol: PMPI_Gather_init
OSError: /DATOS/home/edu/anaconda3/envs/mfix-23.4/bin/…/lib/libmpi_mpifh.so.40: undefined symbol: PMPI_Gather_init
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[53690,1],0]
Exit code: 1
On the other hand, if I open the GUI and I try to compile from there I am not even able to compile and I am getting the error message attached. ERROR.txt (3.1 KB)
What could be happening? I have tried to install/uninstall both Miniforge3 and Anaconda3 several times and I am stuck in the same point with both. I have been able to run the simulations in this very same computer with previous versions of MFiX (and Anaconda3) without any issue.
The Fortran compiler
"/apps/OpenMPI/4.1.4-GCC-11.3.0/bin/mpifort"
is not able to compile a simple test program.
Because of frequent issues with MPI installations on user systems, we bundle a tested and compatible version of openMPI and gfortran/mpifort along with MFiX. The build should be using something like ~/miniforge3/envs/mfix-23.4/bin/mpifort not the one in /apps/OpenMPI. Running mamba activate mfix-23.4 should put miniforge3/envs/mfix-23.4/bin in your $PATH ahead of everything else. So why is /apps/OpenMPI/4.1.4-GCC-11.3.0/bin getting picked up? Did you do something explicit to add this? If so, skip that step.
If you’re still having problems, please do mamba activate mfix-23.4 and then run the command env and send me the output.
Yes, it seems that there was some issue with the path. I am still unable to make it work from the GUI and getting the same error, but I have managed to make it work from the terminal (and I am using that computer only remotely). For the moment I would say that the problem is solved. I will dig again into it in case I need the GUI in the future.
Thank you again for your help and have a nice weekend,
Eduardo
Dear Charles，
I think I’m experiencing a similar problem for mfix-23.4. someone say it’s caused by the file “CMakeTestFortranCompiler.cmake”, but I don’t know exactly how to solve it, can you help me to check it out?
Thank you！
Tong
Note that setting up the mfix-23.4 environment should have put $CONDA_PREFIX/bin at the head of your PATH environment variable. How is /usr/lib64/openmpi/bin getting in there?
Thanks for replying, but sorry I still haven’t solved this environment variable problem, it might be due to my unfamiliarity with linux commands.
If it’s easier for you, could you explain in more detail?
Hi there,
I’m facing quite similar issues. When using an MFiX version below 23.4 the solver building works just fine. Now, with 23.4., I’m receiving the same error messages as @NJIFE . Could the reason be that I’m still using the conda environment and not mamba?
And my Path looks like this: /home/fritzi/anaconda3/bin:/home/fritzi/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
